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Barack Obama has expressed his “profound regret” over a drone strike that killed two innocent hostages – an American and Italian – being held captive by al-Qaida, before praising what he claimed was his administration’s exceptionally transparent response to the tragedy.

The US president spoke shortly after the White House announced that intelligence officials had concluded that the January counter-terrorism operation had “accidentally” killed Dr Warren Weinstein, a US government aid worker, and Giovanni Lo Porto, an Italian aid worker.

The hostages, both of whom had been in al-Qaida captivity for more than two years, were killed during a US strike against an al-Qaida compound in the border region ofAfghanistan and Pakistan.

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Giovanni Lo Porto (L) and Warren Weinstein, the Italian and American hostages killed in the US attack.

Separately, the White House also disclosed that it had mistakenly killed two other Americans, both of whom were suspected of being high-level al-Qaida members but had not been specifically targeted.

Obama did not mention the two American al-Qaida members in the statement from the White House, in which he sought to explain how his counter-terrorism strike could have take the lives of two hostages. Neither did he use the word “drone”.

“As president and as commander-in-chief, I take full responsibility of all of our counter-terrorism operations, including the one that inadvertently took the lives of Warren and Giovanni,” Obama said. “I profoundly regret what happened. On behalf of the United States government, I offer our deepest apologies to their families.”

Yet the president struck a surprisingly defiant tone, insisting that his administration had acted on the best intelligence available at the time and claiming that his decision to declassify the operation and initiate a review was a sign of American exceptionalism.

He said he had decided to make the existence of the operation public because Weinstein and Lo Porto’s families “deserve to know the truth” and “the United States is a democracy, committed to openness, in good times and in bad”.

Weinstein was kidnapped by al-Qaida in 2011. Lo Porto had been a hostage of the terrorist group since 2012.

While Obama praised himself for declassifying news of the mistaken strike, secrecy still surrounds the vast majority of drone strikes that one senator estimated in 2013 hadkilled 4,700 people.

This was only the second time, following a presidential speech that year, that Obama has acknowledged killing innocents. These have included a 16-year-old boy with US citizenship.

Critics have lambasted Obama for conducting a counter-terrorism war stretching around the globe almost entirely in secret.

The American Civil Liberties Union in March sued the Obama administration, which has proclaimed itself the most transparent in history, for disclosure of critical legal documents underpinning what the administration calls its “targeted killing” program – including the criteria for placement on a list permitting the US to kill people, including its own citizens, without trial.

Obama’s admission regarding the deaths of Weinstein and Lo Porto is likely to intensify criticism of the president’s worldwide drone strikes, conducted by the CIA and the military’s Joint Special Operations Command. A recent analysis by human-rights group Reprieve estimated that US drone strikes intending to target 41 men had killed 1,147 people as of November.

US officials insist the operations are “targeted” and cause minimal civilian casualties.

In his statement from the White House Obama said that at the time of the operation that killed Weinstein and Lo Porto intelligence indicated that “this was an al-Qaida compound, that no civilians were present, and that capturing these terrorists was not possible”.

He added: “And we do believe that the operation did take out dangerous members of al-Qaida.”

One of the al-Qaida operatives killed in the same operation against the compound, the White House said separately, was Ahmed Farouq, an American whom it called a “leader” of the terrorist group.

The Obama administration also disclosed that, in a separate operation that also took place in the region in January, it killed a second American member of al-Qaida: Adam Gadahn.

The two American al-Qaida members were not, however, deliberately targeted. Instead, the White House indicated they, too, were killed by accident. “Neither was specifically targeted, and we did not have information indicating their presence at the sites of these operations,” the White House said.

For years, Gadahn was al-Qaida’s premier American member – his nom de guerre was “Azzam the American” – and a fixture of its pre-social-media English-language propaganda. A former heavy-metal fan from California born in 1978, Gadahn joined al-Qaida around the turn of the century after physically attacking an Orange County imamfor insufficient piety.

Obama spoke with Weinstein’s wife, Elaine, and the Italian prime minister, Matteo Renzi, on Tuesday. “As a husband and a father I cannot begin to imagine the anguish that the Weinstein and Lo Porto families are enduring today,” he said. “I realise that there are no words that can ever equal their loss. There is nothing that I can ever say or do to ease their heartache.”

But the president blamed the deaths of the innocent hostages on “the fog of war” and maintained that his response to the tragedy showed his administration’s transparency.

“What we did not know, tragically, is that al-Qaida was hiding the presence of Warren and Giovanni in this same compound. It is a cruel and bitter truth that in the fog of war generally, and in our fight against terrorists specifically, mistakes – sometimes deadly mistakes – can occur,” he said.

“But one of the things that sets America apart from many other nations, one of the things that makes us exceptional, is our willingness to confront squarely our imperfections and to learn from our mistakes.”

Weinstein’s wife Elaine said in a statement their family was “devastated” by the news of his death, and criticised the response of the US government to his abduction.

Elaine Weinstein stressed her husband’s captors “bear ultimate responsibility” for his death, but said the Pakistani government had treated his captivity as “more of an annoyance than a priority”, and described the assistance the family received from the US government as “inconsistent and disappointing”.

“We hope that my husband’s death and the others who have faced similar tragedies in recent months will finally prompt the US government to take its responsibilities seriously, and establish a coordinated and consistent approach to supporting hostages and their families,” she said.

Speaking from Palermo, where Lo Porto was from, his mother Giusy was quoted as saying she did not want to speak to reporters. “Leave me alone to my pain,” she told the Italian news agency Ansa. Her Facebook page was covered with photographs of Lo Porto from a happier time.

“Italy extends its deepest condolences to the family of Giovanni Lo Porto,” prime minister Renzi said in a statement. He had personally been informed of the news by Obama on Wednesday, just days after the two leaders met in Washington. “I express deep sorry for the death of an Italian, who has dedicated his life to serving others,” he added. Lo Porto’s family was notified of his death by Italy’s crisis unit.

In a separate statement, Obama’s press secretary, Josh Earnest, said the “uniquely tragic” nature of the operation was something the administration would do its best to ensure was not repeated. “To this end, although the operation was lawful and conducted consistent with our counter-terrorism policies, we are conducting a thorough independent review to understand fully what happened and how we can prevent this type of tragic incident in the future,” he added.

Dianne Feinstein, the senior Democrat on the Senate intelligence committee, indicated that the oversight panel had known about the mistaken drone strikes for some time.

“The committee has already been reviewing the specific January operation that led to these deaths, and I now intend to review that operation in greater detail,” Feinstein said.

Despite the details released by the White House – a highly unusual move for a clandestine “counterterrorism operation” – important questions remain.

Although it is assumed Weinstein and Lo Porto were killed by a drone strike, it is not known precisely when or where it took place, or how many al-Qaida operatives or other civilians were killed in the strike.

The White House said only the operation took place in the operation that killed Weinstein and Lo Porto took place in the border region of Afghanistan and Pakistan in January.

According to media reports on both sides of the border, there were five attacks in Pakistan in January and seven air strikes in Afghanistan.

Although not all of the Afghanistan strikes may have been by unmanned aircraft, the use of drones has increased sharply in the east of the country in recent months as militants have been pushed from their old sanctuaries in Pakistan.

The Obama administration’s decision not to publicly locate the operation in either Afghanistan or Pakistan is probably the result of a longstanding US practice of merging the border areas between the countries for counter-terrorism purposes.

The US has a UN mandate to conduct military operations in Afghanistan; that is not the case for Pakistan, where the US drone campaign is regarded as illegal by some critics.

Saifullah Mahsud, director of the Fata Research Centre in Islamabad, said he heard rumours months ago that two foreign hostages, including an Italian, had been killed by a drone strike at the end of January.

That could suggest Weinstein and Lo Porto were killed in a 28 January strike in Shawal, a thickly forested area of in North Waziristan, a long-standing trouble spot bordering Afghanistan.

The Obama administration also provided only limited information about the deaths of the two American al-Qaida members it said it now believes it also inadvertently killed in January in the same region.

“There is a limit to what the drone can see on the ground,” said Mahsud. “Incidents like these are bound to happen now and then if you don’t have intelligence on the ground.”

Media reports on drone strikes in no-go areas like North Waziristan are often deeply flawed but coverage at the time suggested a mixture of locals and foreign militants were killed in the attack.

Shazad Akbar, a lawyer and anti-drone campaigner, said he believed the strikes took place in Pakistan and they “proved the CIA have no clue who they are killing”.

“If drones are so precise they should be able to see who they are targeting,” Akbar said. “I wouldn’t be surprised if al-Qaida deliberately gave incorrect information to the CIA, they have done it in the past.”